It is sometimes not an easy choice, guest. If the meaning is clear without it, feel free to omit the 'that":

'List all items you wish to purchase.'-- here there is no problem of interpretation, so 'that' can be safely omitted.

'I found you have been omitting your apostrophes' -- We read and listen linearly, so the first three words, 'I found you', may temporarily mislead us; in this case, a 'that' might make the meaning immediately clearer: 'I found that you have been omitting your apostrophes.'

It is usually a matter of style, not correctness, and there will be different opinions as to the clarity in each case. As you say, it is often a sense of 'flow' and no more that will influence the choice.